Starting phenix.real_space_refine on Wed Sep 25 19:51:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/09_2024/5o3t_3743.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/09_2024/5o3t_3743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/09_2024/5o3t_3743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/09_2024/5o3t_3743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/09_2024/5o3t_3743.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o3t_3743/09_2024/5o3t_3743.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 3510 2.51 5 N 1010 2.21 5 O 1040 1.98 5 H 5790 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11360 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "H" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "I" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "J" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 6.06, per 1000 atoms: 0.53 Number of scatterers: 11360 At special positions: 0 Unit cell: (116.48, 114.4, 46.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 1040 8.00 N 1010 7.00 C 3510 6.00 H 5790 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 807.3 milliseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5780 1.03 - 1.22: 10 1.22 - 1.41: 2130 1.41 - 1.60: 3520 1.60 - 1.79: 10 Bond restraints: 11450 Sorted by residual: bond pdb=" C VAL G 363 " pdb=" N PRO G 364 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.11e-02 8.12e+03 1.89e+00 bond pdb=" C VAL F 363 " pdb=" N PRO F 364 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.11e-02 8.12e+03 1.76e+00 bond pdb=" C VAL H 363 " pdb=" N PRO H 364 " ideal model delta sigma weight residual 1.334 1.319 0.014 1.11e-02 8.12e+03 1.70e+00 bond pdb=" C VAL C 363 " pdb=" N PRO C 364 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.11e-02 8.12e+03 1.63e+00 bond pdb=" C VAL J 363 " pdb=" N PRO J 364 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.11e-02 8.12e+03 1.54e+00 ... (remaining 11445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 17684 1.56 - 3.12: 2803 3.12 - 4.69: 383 4.69 - 6.25: 10 6.25 - 7.81: 20 Bond angle restraints: 20900 Sorted by residual: angle pdb=" N LYS I 331 " pdb=" CA LYS I 331 " pdb=" C LYS I 331 " ideal model delta sigma weight residual 108.97 116.78 -7.81 1.82e+00 3.02e-01 1.84e+01 angle pdb=" N LYS E 331 " pdb=" CA LYS E 331 " pdb=" C LYS E 331 " ideal model delta sigma weight residual 108.97 116.78 -7.81 1.82e+00 3.02e-01 1.84e+01 angle pdb=" N LYS C 331 " pdb=" CA LYS C 331 " pdb=" C LYS C 331 " ideal model delta sigma weight residual 108.97 116.75 -7.78 1.82e+00 3.02e-01 1.83e+01 angle pdb=" N LYS A 331 " pdb=" CA LYS A 331 " pdb=" C LYS A 331 " ideal model delta sigma weight residual 108.97 116.75 -7.78 1.82e+00 3.02e-01 1.83e+01 angle pdb=" N LYS G 331 " pdb=" CA LYS G 331 " pdb=" C LYS G 331 " ideal model delta sigma weight residual 108.97 116.74 -7.77 1.82e+00 3.02e-01 1.82e+01 ... (remaining 20895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.52: 4578 10.52 - 21.04: 327 21.04 - 31.56: 195 31.56 - 42.09: 80 42.09 - 52.61: 90 Dihedral angle restraints: 5270 sinusoidal: 3000 harmonic: 2270 Sorted by residual: dihedral pdb=" CA LEU E 315 " pdb=" C LEU E 315 " pdb=" N SER E 316 " pdb=" CA SER E 316 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU F 315 " pdb=" C LEU F 315 " pdb=" N SER F 316 " pdb=" CA SER F 316 " ideal model delta harmonic sigma weight residual -180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU C 315 " pdb=" C LEU C 315 " pdb=" N SER C 316 " pdb=" CA SER C 316 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 5267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 390 0.027 - 0.054: 216 0.054 - 0.081: 114 0.081 - 0.108: 78 0.108 - 0.135: 62 Chirality restraints: 860 Sorted by residual: chirality pdb=" CA LYS C 331 " pdb=" N LYS C 331 " pdb=" C LYS C 331 " pdb=" CB LYS C 331 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE E 328 " pdb=" N ILE E 328 " pdb=" C ILE E 328 " pdb=" CB ILE E 328 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE F 328 " pdb=" N ILE F 328 " pdb=" C ILE F 328 " pdb=" CB ILE F 328 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 857 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 363 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO B 364 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 364 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 364 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 363 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO D 364 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 364 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 364 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 363 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO G 364 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 364 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 364 " -0.024 5.00e-02 4.00e+02 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.91: 171 1.91 - 2.58: 12948 2.58 - 3.26: 33858 3.26 - 3.93: 42845 3.93 - 4.60: 66195 Nonbonded interactions: 156017 Sorted by model distance: nonbonded pdb=" HB3 HIS F 329 " pdb=" HE3 LYS F 331 " model vdw 1.242 2.440 nonbonded pdb=" HB3 HIS B 329 " pdb=" HE3 LYS B 331 " model vdw 1.242 2.440 nonbonded pdb=" HB3 HIS J 329 " pdb=" HE3 LYS J 331 " model vdw 1.242 2.440 nonbonded pdb=" HB3 HIS D 329 " pdb=" HE3 LYS D 331 " model vdw 1.243 2.440 nonbonded pdb=" HB3 HIS H 329 " pdb=" HE3 LYS H 331 " model vdw 1.243 2.440 ... (remaining 156012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 24.510 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 5660 Z= 0.273 Angle : 0.915 7.811 7580 Z= 0.472 Chirality : 0.055 0.135 860 Planarity : 0.005 0.043 960 Dihedral : 10.151 50.514 2160 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % Rotamer: Outliers : 1.56 % Allowed : 3.12 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.47 (0.15), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.12), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 374 PHE 0.007 0.001 PHE D 346 TYR 0.005 0.003 TYR C 310 ARG 0.002 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 360 ILE cc_start: 0.6710 (mp) cc_final: 0.6451 (mt) REVERT: D 360 ILE cc_start: 0.5942 (mp) cc_final: 0.5679 (mt) REVERT: G 331 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7618 (mttt) outliers start: 10 outliers final: 5 residues processed: 154 average time/residue: 0.6309 time to fit residues: 114.3405 Evaluate side-chains 88 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS E 362 HIS G 351 GLN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5660 Z= 0.155 Angle : 0.650 4.617 7580 Z= 0.332 Chirality : 0.051 0.134 860 Planarity : 0.004 0.028 960 Dihedral : 7.764 49.325 764 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 1.72 % Allowed : 9.84 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.01 (0.17), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.13), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 374 PHE 0.020 0.001 PHE J 346 TYR 0.009 0.003 TYR I 310 ARG 0.002 0.000 ARG J 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5585 (OUTLIER) cc_final: 0.5071 (mmmt) REVERT: B 360 ILE cc_start: 0.6882 (mp) cc_final: 0.6637 (mt) REVERT: F 360 ILE cc_start: 0.6885 (mp) cc_final: 0.6611 (mt) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.4830 time to fit residues: 61.6318 Evaluate side-chains 78 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS J 359 ASN J 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5660 Z= 0.145 Angle : 0.581 3.904 7580 Z= 0.299 Chirality : 0.049 0.135 860 Planarity : 0.003 0.025 960 Dihedral : 7.164 48.489 756 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 1.41 % Allowed : 11.88 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.75 (0.18), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.14), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 330 PHE 0.014 0.002 PHE E 346 TYR 0.009 0.002 TYR C 310 ARG 0.003 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5283 (OUTLIER) cc_final: 0.3980 (mmtm) REVERT: B 360 ILE cc_start: 0.6928 (mp) cc_final: 0.6654 (mt) REVERT: F 360 ILE cc_start: 0.6915 (mp) cc_final: 0.6688 (mt) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.4072 time to fit residues: 48.0894 Evaluate side-chains 78 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain H residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5660 Z= 0.106 Angle : 0.536 3.964 7580 Z= 0.273 Chirality : 0.049 0.129 860 Planarity : 0.003 0.024 960 Dihedral : 6.612 48.913 752 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.88 % Allowed : 11.88 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.47 (0.19), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.14), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 330 PHE 0.010 0.001 PHE E 346 TYR 0.009 0.002 TYR C 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5156 (OUTLIER) cc_final: 0.3886 (mmtm) REVERT: B 360 ILE cc_start: 0.6931 (mp) cc_final: 0.6656 (mt) REVERT: F 360 ILE cc_start: 0.6765 (mp) cc_final: 0.6536 (mt) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 0.4114 time to fit residues: 45.6261 Evaluate side-chains 77 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 ASN F 362 HIS ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 362 HIS ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5660 Z= 0.190 Angle : 0.605 4.855 7580 Z= 0.312 Chirality : 0.050 0.128 860 Planarity : 0.003 0.028 960 Dihedral : 7.206 52.894 752 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.94 % Favored : 86.06 % Rotamer: Outliers : 2.19 % Allowed : 12.97 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.45 (0.19), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 374 PHE 0.016 0.002 PHE E 346 TYR 0.010 0.003 TYR E 310 ARG 0.002 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5635 (OUTLIER) cc_final: 0.4232 (mmtm) REVERT: B 360 ILE cc_start: 0.7171 (mp) cc_final: 0.6882 (mt) REVERT: I 363 VAL cc_start: 0.8560 (t) cc_final: 0.8241 (t) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.4256 time to fit residues: 48.7774 Evaluate side-chains 82 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 65 optimal weight: 0.2980 chunk 7 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5660 Z= 0.111 Angle : 0.537 4.570 7580 Z= 0.274 Chirality : 0.049 0.143 860 Planarity : 0.003 0.026 960 Dihedral : 6.808 54.046 752 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.19 % Allowed : 14.06 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.009 0.001 PHE E 346 TYR 0.009 0.002 TYR A 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5416 (OUTLIER) cc_final: 0.4094 (mmtm) REVERT: B 360 ILE cc_start: 0.7177 (mp) cc_final: 0.6898 (mt) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.4378 time to fit residues: 50.0682 Evaluate side-chains 81 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5660 Z= 0.155 Angle : 0.552 3.874 7580 Z= 0.283 Chirality : 0.049 0.172 860 Planarity : 0.003 0.028 960 Dihedral : 6.908 57.377 752 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 2.19 % Allowed : 14.84 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.008 0.001 PHE F 346 TYR 0.008 0.002 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5544 (OUTLIER) cc_final: 0.4811 (mmmt) REVERT: B 360 ILE cc_start: 0.7140 (mp) cc_final: 0.6930 (mt) outliers start: 14 outliers final: 11 residues processed: 85 average time/residue: 0.4265 time to fit residues: 47.4309 Evaluate side-chains 85 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 0.0970 chunk 58 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5660 Z= 0.107 Angle : 0.515 3.465 7580 Z= 0.262 Chirality : 0.049 0.148 860 Planarity : 0.003 0.027 960 Dihedral : 6.760 59.570 752 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.34 % Allowed : 14.84 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.08 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.010 0.001 PHE F 346 TYR 0.009 0.002 TYR A 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5386 (OUTLIER) cc_final: 0.4111 (mmtm) REVERT: D 354 ILE cc_start: 0.5115 (mm) cc_final: 0.4904 (mt) outliers start: 15 outliers final: 14 residues processed: 87 average time/residue: 0.4177 time to fit residues: 46.8844 Evaluate side-chains 80 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.7145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5660 Z= 0.178 Angle : 0.566 4.556 7580 Z= 0.289 Chirality : 0.050 0.130 860 Planarity : 0.003 0.026 960 Dihedral : 6.960 58.747 752 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 2.66 % Allowed : 14.84 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.15), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 374 PHE 0.022 0.001 PHE I 346 TYR 0.009 0.003 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5624 (OUTLIER) cc_final: 0.4738 (mmmt) outliers start: 17 outliers final: 15 residues processed: 96 average time/residue: 0.4085 time to fit residues: 51.0394 Evaluate side-chains 93 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.7349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5660 Z= 0.127 Angle : 0.543 4.397 7580 Z= 0.276 Chirality : 0.049 0.135 860 Planarity : 0.003 0.025 960 Dihedral : 6.799 57.387 752 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 2.34 % Allowed : 15.94 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 330 PHE 0.022 0.001 PHE I 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.5711 (OUTLIER) cc_final: 0.4461 (mmtt) outliers start: 15 outliers final: 13 residues processed: 86 average time/residue: 0.3913 time to fit residues: 43.7971 Evaluate side-chains 87 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain H residue 331 LYS Chi-restraints excluded: chain I residue 356 SER Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS D 362 HIS ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.178735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.129425 restraints weight = 19473.964| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 3.01 r_work: 0.4394 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.4287 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.7504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5660 Z= 0.154 Angle : 0.552 4.424 7580 Z= 0.281 Chirality : 0.049 0.133 860 Planarity : 0.003 0.025 960 Dihedral : 6.501 59.360 748 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.93 % Favored : 85.07 % Rotamer: Outliers : 1.88 % Allowed : 16.88 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.20), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.16), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.021 0.001 PHE I 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3689.15 seconds wall clock time: 65 minutes 44.66 seconds (3944.66 seconds total)